Hello, Lin
I would check the crystal packing to see if there is another molecule missing in your model. You can do this in TURBO program.
1) label each molecule A, B, C and D.
2) write down the interaction of each molecule with neighboring molecules including symmetry-related molecules.
3) sort all interactions and you will find several different kinds of interactions.
4) you would be able to find the missing one based on these interactions.
I had a similar case several years ago. I could find three molecules in one AU using AmoRe and free R factor stays around 37% for the whole model. The problem got solved after I found the fourth molecule. Finally, I found the fourth one have identical orientation to one of original three.
good luck.
yuequan
the University of Chicago
